|
| Status |
Public on Oct 20, 2015 |
| Title |
PCC6803_∆nsiR4_12hCuSO4_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
cells from liquid culture grown for 12 h in presence of 2 µM CuSO4
|
| Organism |
Synechocystis sp. PCC 6803 |
| Characteristics |
genotype/variation: ∆nsiR4
|
| Treatment protocol |
To induce the ectopic expression of NsiR4, 2 µM CuSO4 was added to the cultures.
|
| Growth protocol |
For the generation of nsiR4 mutants, we used the glucose-tolerant strain Synechocystis 6803 (GT-Kazusa) provided from N. Murata (National Institute for Basic Biology, Okazaki, Japan). Cultivation was performed in Cu2+-free BG11 medium buffered with 20 mM TES, pH 8.0 at 30°C under continuous white light illumination of 50–80 μmol quanta m−2 s−1 and gentle agitation. Mutant strains were grown in presence of the corresponding antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Synechocystis 6803 cells were collected by rapid filtration on hydrophilic polyethersulfone filters (Pall Supor 800 Filter, 0.8 µm). Filters covered with cells were dissolved in 1 ml PGTX (Pinto et al., 2009; BMC Mol Biol 10: 79) and RNA was extracted as described (Hein et al., 2013; RNA Biol 10: 852–864).
|
| Label |
Cy3
|
| Label protocol |
The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.
|
| |
|
| Hybridization protocol |
The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA
|
| Scan protocol |
Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays
|
| Data processing |
Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.
|
| |
|
| Submission date |
Oct 08, 2015 |
| Last update date |
Oct 20, 2015 |
| Contact name |
Stephan Klähn |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Freiburg
|
| Department |
Institute of Biology III
|
| Lab |
Genetics & Experimental Bioinformatics
|
| Street address |
Schänzlestrasse 1
|
| City |
Freiburg |
| State/province |
Baden-Würtemberg |
| ZIP/Postal code |
79104 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15867 |
| Series (1) |
| GSE73840 |
The sRNA NsiR4 is involved in nitrogen assimilation control in cyanobacteria by targeting glutamine synthetase inactivating factor IF7 |
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